This question is entitled If there is an infinite number of universes doesn't that mean there is a universe where there is not an infinite number of parallel universes?. I downvoted this question and voted to close. I also left a comment that said:
If there are an infinite number of triangles in the plane, doesn't that mean there is a triangle where there is not an infinite number of triangles?
It seems to me that this was a pretty useful analogy for understanding what was wrong with the question (or at least one of the things that was wrong with the question), viz: universes are not elements of other universes, any more than triangles are elements of other triangles. I also think that the slightly flippant tone in no way detracted from the usefulness of the comment and in fact probably contributed toward making the point clear. This comment was deleted. I do not think it should have been, particularly because there have been quite a few posts on meta requesting that downvoters should attempt to leave informative comments.
One could perhaps argue that this comment was cryptic. But I think it was cryptic only in the sense that it's "cryptic" to offer hints rather than solutions to homework problems. It invites the OP to do a little thinking.
I realize there have been a great many discussions about comment deletion. Many of those have centered around long comment threads. This post, by contrast, is about the deletion of single comments that, by way of analogy, invite the OP to reflect for a moment or two on the internal logic of the question.
Another example: This question on meta asks
Why don't some questions on PSE have any answers for the past many years with many high votes? ... Do they really don't have answers like proof of Goldabach's conjecture or yet their answers are very hard?
I left a comment that said something like:
Why do some roads have so little traffic? Are they just too hard to get to, like Mars?
Once again, I believe the comment makes a point that is likely to be useful to the OP, and that the light-hearted tone does not detract from that usefulness. This comment was upvoted several times.
This sort of deletion has happened several times over the past couple of years, though I haven't kept records so I have no other examples at my fingertips. Many of the deleted comments were heavily upvoted. I hope the moderators can be encouraged to tread a little more lightly here.
Edited to add: Some of the answers below suggest that it would be better to turn these comments into answers. Here is why I don't think that's advisable:
I leave this kind of comment on posts where I think that the OP is making simple and fundamental errors in reasoning. I think most of those posts should be closed and that when a post should be closed, it should not receive answers that might encourage the OP to continue posting without thinking.
At the same time, I think it's helpful to the OP to point out those errors in reasoning --- and that one of the most effective way to point them out is to translate the same reasoning into another context where it's quite clear that the reasoning has gone haywire.
So in short: I want to be helpful, but I don't want to be encouraging (in the limited sense that I don't want to encourage future ill-considered posts). I think that a) a brief comment pointing out the problem (together with a vote to close) is a good way to further both goals, and b) that often the best brief comment is one that offers an analogy for the OP to ponder. If the OP is not in a pondering mood, the analogy might be lost, but often it will make a light go on. I often use this kind of analogy in the classroom. It seems pretty effective with reasonably good students who have made thoughtless errors, and entirely ineffective with students who are making no effort anyway, but I'm not sure there's any good alternative in those cases, and at the very least no harm is done.